Mothur bioinformatics pipeline

Summary report

Metadata profiling

Compact structure of metadata

tibble [133 × 7] (S3: tbl_df/tbl/data.frame)
 $ sample_id  : chr [1:133] "SRR10245277" "SRR10245278" "SRR10245279" "SRR10245280" ...
 $ ecosystem  : chr [1:133] "Serengeti" "Serengeti" "Serengeti" "Selous" ...
 $ isolate    : chr [1:133] "Wildebeest" "Pig" "Eland" "Gazelle" ...
 $ latitude   : num [1:133] -2.15 -2.15 -2.15 -9 -9 ...
 $ longitude  : num [1:133] 34.7 34.7 34.7 37.5 37.5 ...
 $ milionbases: num [1:133] 189 261 155 156 105 188 157 122 128 240 ...
 $ description: chr [1:133] "Connochaetes taurinus" "Suidae" "Tragelaphus oryx" "Gazella" ...



Original OTU table

# A tibble: 6 × 591
  label Group  numOtus Otu001 Otu002 Otu003 Otu004 Otu005 Otu006 Otu007 Otu008
  <dbl> <chr>    <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
1  0.03 F3D0       588    500    296    394    404    633    168    356    164
2  0.03 F3D1       588    352    304    189     64     73    127    117    174
3  0.03 F3D141     588    388    325    303    482    426    205    279    327
4  0.03 F3D142     588    244    252    142    152    253    201    193     81
5  0.03 F3D143     588    189    150    173    206    310    116    183     92
6  0.03 F3D144     588    347    237    260    316    469    132    282     36
# … with 580 more variables: Otu009 <dbl>, Otu010 <dbl>, Otu011 <dbl>,
#   Otu012 <dbl>, Otu013 <dbl>, Otu014 <dbl>, Otu015 <dbl>, Otu016 <dbl>,
#   Otu017 <dbl>, Otu018 <dbl>, Otu019 <dbl>, Otu020 <dbl>, Otu021 <dbl>,
#   Otu022 <dbl>, Otu023 <dbl>, Otu024 <dbl>, Otu025 <dbl>, Otu026 <dbl>,
#   Otu027 <dbl>, Otu028 <dbl>, Otu029 <dbl>, Otu030 <dbl>, Otu031 <dbl>,
#   Otu032 <dbl>, Otu033 <dbl>, Otu034 <dbl>, Otu035 <dbl>, Otu036 <dbl>,
#   Otu037 <dbl>, Otu038 <dbl>, Otu039 <dbl>, Otu040 <dbl>, Otu041 <dbl>, …

Tidy OTU long table

# A tibble: 6 × 3
  sample_id otu    count
  <chr>     <chr>  <dbl>
1 F3D0      otu001   500
2 F3D0      otu002   296
3 F3D0      otu003   394
4 F3D0      otu004   404
5 F3D0      otu005   633
6 F3D0      otu006   168

Tidy OTU wide table

# A tibble: 6 × 28
  otu     F3D0  F3D1 F3D141 F3D142 F3D143 F3D144 F3D145 F3D146 F3D147 F3D148
  <chr>  <dbl> <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
1 otu001   500   352    388    244    189    347    568    272   1316    751
2 otu002   296   304    325    252    150    237    439    201   1090    650
3 otu003   394   189    303    142    173    260    461    225    820    521
4 otu004   404    64    482    152    206    316    527    370   1053    829
5 otu005   633    73    426    253    310    469    665    397   1621   1230
6 otu006   168   127    205    201    116    132    362    193    546    499
# … with 17 more variables: F3D149 <dbl>, F3D2 <dbl>, F3D3 <dbl>, F3D5 <dbl>,
#   F3D6 <dbl>, F3D7 <dbl>, F3D8 <dbl>, F3D9 <dbl>, M1D0 <dbl>, M1D1 <dbl>,
#   M1D2 <dbl>, Mock1 <dbl>, Mock2 <dbl>, Mock3 <dbl>, Water1 <dbl>,
#   Water2 <dbl>, Water3 <dbl>
[1] "Dimension of the phylotype table table is 588 rows and 28 columns"

Original taxonomy table

# A tibble: 6 × 3
  OTU     Size Taxonomy                                                         
  <chr>  <dbl> <chr>                                                            
1 Otu001 13221 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(…
2 Otu002 10070 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(…
3 Otu003  8352 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(…
4 Otu004  8305 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(…
5 Otu005  8251 Bacteria(100);Bacteroidetes(100);Bacteroidia(99);Bacteroidales(9…
6 Otu006  7973 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(…

Tidy taxonomy table

# A tibble: 6 × 8
  otu    pretty_otu kingdom  phylum        class       order        family genus
  <chr>  <chr>      <chr>    <chr>         <chr>       <chr>        <chr>  <chr>
1 otu001 OTU 1      Bacteria Bacteroidetes Bacteroidia Bacteroidal… Bacte… Bact…
2 otu002 OTU 2      Bacteria Bacteroidetes Bacteroidia Bacteroidal… Bacte… Bact…
3 otu003 OTU 3      Bacteria Bacteroidetes Bacteroidia Bacteroidal… Bacte… Bact…
4 otu004 OTU 4      Bacteria Bacteroidetes Bacteroidia Bacteroidal… Bacte… Bact…
5 otu005 OTU 5      Bacteria Bacteroidetes Bacteroidia Bacteroidal… Bacte… Bact…
6 otu006 OTU 6      Bacteria Bacteroidetes Bacteroidia Bacteroidal… Bacte… Bact…